[BiO BB] Re: question on clustering

William Thompson thompson at wadsworth.org
Fri Aug 6 13:24:35 EDT 2004

You might want to look into R http://www.r-project.org/ R is a programming tool 
for statistics and data analysis. R has a fairly complete clustering package. 
It's free, robust and there are lots of web resources for it.


Bill Thompson, PhD
Bioinformatics Center
NYS Department of Health
Center for Medical Science, rm 2006
150 New Scotland Avenue
Albany, New York 12208
(518) 486-7882

> Hi all,
> I have a question that concerns my MSc project. I am trying to cluster 30
> CCP-modules (Complement Receptor 1) after having used a novel approach that
> looks at the electrostatic surfaces. I have reached the stage where I have
> obtained a similarity matrix of 30 by 30 filled with positive scores. The
> higher a score the more similar two modules are. For example, if matrix entry
> (3,6) = 13 and entry (3,8) = 24 then module 3 is more similar to module 8 than
> to module 6 due to a higher score. My problem now is to cluster these 30
> modules based on this one similarity matrix. I am not used to have to cluster
> small datasets or in this case a similarity matrix and not having training
> data. I have searched around a lot on Google for programs that could cluster 
> modules using the similarity matrix but so far I have not found anything very
> helpful. Does anyone know of a program (preferably free software) that could
> help me out here, or another way which I could easily implement myself in a
> script, that would be valid? I would really appreciate all replies to this
> message and thank you all already for looking at this and thinking about this.
> Thanks and regards,
> Floris

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